cAMP responsive element binding protein-1

Overview
NamecAMP responsive element binding protein-1 (AFJ24841.1)
Smed IDSMED30006028
Length (bp)1110
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast Population

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

 

Overview

 

Single cell RNA-seq of pluripotent neoblasts and its early progenies


We isolated X1 neoblasts cells enriched in high piwi-1 expression (Neoblast Population), and profiled ∼7,614 individual cells via scRNA-seq. Unsupervised analyses uncovered 12 distinct classes from 7,088 high-quality cells. We designated these classes Nb1 to Nb12 and ordered them based on high (Nb1) to low (Nb12) piwi-1 expression levels. We further defined groups of genes that best classified the cells parsed into 12 distinct cell clusters to generate a scaled expression heat map of discriminative gene sets for each cluster. Expression of each cluster’s gene signatures was validated using multiplex fluorescence in situ hybridization (FISH) co-stained with piwi-1 and largely confirmed the cell clusters revealed by scRNA-seq.

We also tested sub-lethal irradiation exposure. To profile rare pluripotent stem cells (PSCs) and avoid interference from immediate progenitor cells, we determined a time point after sub-lethal irradiation (7 DPI) with minimal piwi-1+ cells, followed by isolation and single-cell RNA-seq of 1,200 individual cells derived from X1 (Piwi-1 high) and X2 (Piwi-1 low) cell populations (Sub-lethal Irradiated Surviving X1 and X2 Cell Population)



Explore this single cell expression dataset with our NB Cluster Shiny App



 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of cAMP responsive element binding protein-1 (SMED30006028) t-SNE clustered cells

Violin plots show distribution of expression levels for cAMP responsive element binding protein-1 (SMED30006028) in cells (dots) of each of the 12 neoblast clusters.

 

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Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of cAMP responsive element binding protein-1 (SMED30006028) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for cAMP responsive element binding protein-1 (SMED30006028) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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Embryonic Expression

Davies et. al., 2017

Hover the mouse over a column in the graph to view average RPKM values per sample.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult.
For further information about sample preparation and analysis for the single animal RNA-Seq experiment, please refer to the Materials and Methods

 

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Anatomical Expression

PAGE et. al., 2020



SMED30006028

has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGE



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X2 cellSMED30006028SMESG000052278.1 SMESG000012628.1 SmedASXL_004708SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of cAMP responsive element binding protein-1 vs. TrEMBL
Match: I1ZII7 (cAMP responsive element binding protein-1 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 205.297 bits (521), Expect = 4.272e-62
Identity = 139/141 (98.58%), Postives = 139/141 (98.58%), Query Frame = 2 
Query:  485 SCXXXXXXXXXXXXQFSPCPQIISHRNDLPSVFDPKYTLNQKSGILNDESXXXXXXXXXXXXXXXXXXXXXXQHVEVLESKLQKQQEAISLLKNKMKLVLNEMMRLDEYITKTDIPHCDLKDFRQIKDDVAVFLDLVESES 907
            SCTNTITIPNTTATQFSPCPQIISHRNDLPSVFDPKYTLNQKSGILNDESRRLERKREKNREAARKCRERKNQHVEVLESKLQKQQEAIS LKNKMKLVLNEMMRLDEYITKTDIPHCDLKDF QIKDDVAVFLDLVESES
Sbjct:   11 SCTNTITIPNTTATQFSPCPQIISHRNDLPSVFDPKYTLNQKSGILNDESRRLERKREKNREAARKCRERKNQHVEVLESKLQKQQEAISQLKNKMKLVLNEMMRLDEYITKTDIPHCDLKDFSQIKDDVAVFLDLVESES 151
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BLAST of cAMP responsive element binding protein-1 vs. Planmine SMEST
Match: SMESG000052278.1 (SMESG000052278.1)

HSP 1 Score: 425.246 bits (1092), Expect = 6.024e-150
Identity = 296/296 (100.00%), Postives = 296/296 (100.00%), Query Frame = 2 
Query:   20 MQHLFKSEKIEHDSYLQNNFSFNPNSXXXXXXXXXXXXXXXXXXXXXXXVSNISPQSNISDLFSQSSNAINEDYKSNPNSLNDDILSVSQQNVVNNSPAGIDLNANLTNAILFHPNVDPYSSNTFVPANISPGLTLIQSCXXXXXXXXXXXXXXXSCXXXXXXXXXXXXQFSPCPQIISHRNDLPSVFDPKYTLNQKSGILNDESXXXXXXXXXXXXXXXXXXXXXXQHVEVLESKLQKQQEAISLLKNKMKLVLNEMMRLDEYITKTDIPHCDLKDFRQIKDDVAVFLDLVESES 907
            MQHLFKSEKIEHDSYLQNNFSFNPNSINAEINNEIFGINIINTTNCQNTVSNISPQSNISDLFSQSSNAINEDYKSNPNSLNDDILSVSQQNVVNNSPAGIDLNANLTNAILFHPNVDPYSSNTFVPANISPGLTLIQSCPNNNYMPYPNNYQYNSCTNTITIPNTTATQFSPCPQIISHRNDLPSVFDPKYTLNQKSGILNDESRRLERKREKNREAARKCRERKNQHVEVLESKLQKQQEAISLLKNKMKLVLNEMMRLDEYITKTDIPHCDLKDFRQIKDDVAVFLDLVESES
Sbjct:    1 MQHLFKSEKIEHDSYLQNNFSFNPNSINAEINNEIFGINIINTTNCQNTVSNISPQSNISDLFSQSSNAINEDYKSNPNSLNDDILSVSQQNVVNNSPAGIDLNANLTNAILFHPNVDPYSSNTFVPANISPGLTLIQSCPNNNYMPYPNNYQYNSCTNTITIPNTTATQFSPCPQIISHRNDLPSVFDPKYTLNQKSGILNDESRRLERKREKNREAARKCRERKNQHVEVLESKLQKQQEAISLLKNKMKLVLNEMMRLDEYITKTDIPHCDLKDFRQIKDDVAVFLDLVESES 296
[Close]
BLAST of cAMP responsive element binding protein-1 vs. Planmine SMEST
Match: SMESG000012628.1 (SMESG000012628.1)

HSP 1 Score: 422.55 bits (1085), Expect = 7.700e-149
Identity = 295/296 (99.66%), Postives = 295/296 (99.66%), Query Frame = 2 
Query:   20 MQHLFKSEKIEHDSYLQNNFSFNPNSXXXXXXXXXXXXXXXXXXXXXXXVSNISPQSNISDLFSQSSNAINEDYKSNPNSLNDDILSVSQQNVVNNSPAGIDLNANLTNAILFHPNVDPYSSNTFVPANISPGLTLIQSCXXXXXXXXXXXXXXXSCXXXXXXXXXXXXQFSPCPQIISHRNDLPSVFDPKYTLNQKSGILNDESXXXXXXXXXXXXXXXXXXXXXXQHVEVLESKLQKQQEAISLLKNKMKLVLNEMMRLDEYITKTDIPHCDLKDFRQIKDDVAVFLDLVESES 907
            MQHLFKSEKIEHDSYLQNNFSFNPNSINAEINNEIFGINIINTTNCQNTVSNISPQSNISDLFSQSSNAINEDYKSNPNSLNDDILSVSQQNVVNNSPAGIDLNANLTNAILFHPNVDPYSSNTFVPANISPGLTLIQSCPNNNYMPYPNNYQYNSCTNTITIPNTTATQFSPCPQIISHRNDLPSVFDPKYTLNQKSGILNDESRRLERKREKNREAARKCRERKNQHVEVLESKLQKQQEAIS LKNKMKLVLNEMMRLDEYITKTDIPHCDLKDFRQIKDDVAVFLDLVESES
Sbjct:    1 MQHLFKSEKIEHDSYLQNNFSFNPNSINAEINNEIFGINIINTTNCQNTVSNISPQSNISDLFSQSSNAINEDYKSNPNSLNDDILSVSQQNVVNNSPAGIDLNANLTNAILFHPNVDPYSSNTFVPANISPGLTLIQSCPNNNYMPYPNNYQYNSCTNTITIPNTTATQFSPCPQIISHRNDLPSVFDPKYTLNQKSGILNDESRRLERKREKNREAARKCRERKNQHVEVLESKLQKQQEAISQLKNKMKLVLNEMMRLDEYITKTDIPHCDLKDFRQIKDDVAVFLDLVESES 296
The following BLAST results are available for this feature:
BLAST of cAMP responsive element binding protein-1 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of cAMP responsive element binding protein-1 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of cAMP responsive element binding protein-1 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of cAMP responsive element binding protein-1 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of cAMP responsive element binding protein-1 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of cAMP responsive element binding protein-1 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of cAMP responsive element binding protein-1 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of cAMP responsive element binding protein-1 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
I1ZII74.272e-6298.58cAMP responsive element binding protein-1 OS=Schmi... [more]
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BLAST of cAMP responsive element binding protein-1 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of cAMP responsive element binding protein-1 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of cAMP responsive element binding protein-1 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of cAMP responsive element binding protein-1 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of cAMP responsive element binding protein-1 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of cAMP responsive element binding protein-1 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000052278.16.024e-150100.00SMESG000052278.1[more]
SMESG000012628.17.700e-14999.66SMESG000012628.1[more]
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Cross References
External references for this transcript
DatabaseAccession
SmedGD GBrowseSMED30006028
GenBankAFJ24841.1
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30006028 ID=SMED30006028|Name=cAMP responsive element binding protein-1|organism=Schmidtea mediterranea sexual|type=transcript|length=1110bp
CTCATTGTATGACTAACATATGCAACATTTATTTAAATCTGAAAAAATAG
AGCATGACTCATATTTACAGAATAATTTCTCATTTAATCCCAATTCTATT
AATGCAGAAATAAACAATGAAATTTTTGGGATAAATATTATTAATACTAC
TAATTGCCAAAATACTGTTTCAAACATTTCTCCGCAATCTAATATATCTG
ATCTATTTTCTCAGTCTTCGAATGCAATTAACGAAGATTACAAGTCTAAT
CCTAACAGCTTAAATGATGACATTTTATCAGTTTCACAACAGAATGTTGT
CAATAATTCACCAGCTGGAATTGATTTAAATGCTAATTTGACTAACGCAA
TTTTATTTCACCCAAATGTGGATCCATATAGTTCGAATACTTTTGTACCA
GCAAATATTTCACCAGGTTTAACTCTTATTCAATCATGCCCTAATAATAA
TTATATGCCATATCCAAATAATTATCAATATAATAGTTGCACAAATACTA
TAACTATTCCCAACACCACTGCGACTCAGTTCAGTCCATGCCCCCAAATA
ATTTCACATCGTAATGACTTGCCTTCAGTTTTTGATCCGAAATACACCTT
GAACCAAAAGTCTGGTATTCTTAATGATGAAAGCAGACGGCTAGAACGTA
AGCGTGAAAAAAATCGAGAAGCTGCAAGAAAATGTCGTGAAAGAAAGAAT
CAACATGTTGAGGTATTAGAGAGCAAATTGCAAAAGCAACAAGAAGCTAT
ATCACTATTAAAGAACAAAATGAAATTGGTTCTCAATGAAATGATGAGAC
TGGATGAATATATAACCAAAACTGACATACCTCATTGTGATTTGAAAGAT
TTCAGACAAATCAAAGATGATGTCGCGGTTTTCTTGGATTTAGTAGAATC
AGAATCTTAGCATATGTATTTAATATAAATATCGAGTGCATTTAAATTGC
GATTTTTCTGGAATATTTTTCTATTAACATTTTTGCTAAAGTTTGCTTTT
TTAGAATTCAATTTTTTAATATATTAGTGCCTGCCATTATTTCAATTTGC
TTTTCATTTGTAATTTTGTAGGATTCACTACCTCGCTTTTCTATTTGAAT
AATGTTGCGC
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protein sequence of SMED30006028-orf-1

>SMED30006028-orf-1 ID=SMED30006028-orf-1|Name=SMED30006028-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=297bp
MQHLFKSEKIEHDSYLQNNFSFNPNSINAEINNEIFGINIINTTNCQNTV
SNISPQSNISDLFSQSSNAINEDYKSNPNSLNDDILSVSQQNVVNNSPAG
IDLNANLTNAILFHPNVDPYSSNTFVPANISPGLTLIQSCPNNNYMPYPN
NYQYNSCTNTITIPNTTATQFSPCPQIISHRNDLPSVFDPKYTLNQKSGI
LNDESRRLERKREKNREAARKCRERKNQHVEVLESKLQKQQEAISLLKNK
MKLVLNEMMRLDEYITKTDIPHCDLKDFRQIKDDVAVFLDLVESES*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002111X2 cell
Vocabulary: INTERPRO
TermDefinition
IPR004827bZIP
Vocabulary: biological process
TermDefinition
GO:0006355regulation of transcription, DNA-templated
Vocabulary: molecular function
TermDefinition
GO:0043565sequence-specific DNA binding
GO:0003700transcription factor activity, sequence-specific DNA binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 201..257
NoneNo IPR availableGENE3DG3DSA:1.20.5.170coord: 207..267
e-value: 2.1E-8
score: 36.3
NoneNo IPR availablePANTHERPTHR11462:SF35TRANSCRIPTION FACTOR AP-1coord: 46..250
NoneNo IPR availablePANTHERPTHR11462JUN TRANSCRIPTION FACTOR-RELATEDcoord: 46..250
NoneNo IPR availableCDDcd14686bZIPcoord: 209..258
e-value: 3.74972E-12
score: 57.9405
NoneNo IPR availableSUPERFAMILYSSF57959Leucine zipper domaincoord: 207..262
IPR004827Basic-leucine zipper domainSMARTSM00338brlzneucoord: 203..267
e-value: 4.2E-5
score: 33.0
IPR004827Basic-leucine zipper domainPFAMPF07716bZIP_2coord: 209..254
e-value: 2.3E-6
score: 27.6
IPR004827Basic-leucine zipper domainPROSITEPS00036BZIP_BASICcoord: 210..225
IPR004827Basic-leucine zipper domainPROSITEPS50217BZIPcoord: 205..268
score: 10.3